SVA: software for annotating and visualizing sequenced human genomes

被引：50

作者：

Ge, Dongliang ^{[1
,2
]}

Ruzzo, Elizabeth K. ^{[1
]}

Shianna, Kevin V. ^{[1
]}

He, Min ^{[1
]}

Pelak, Kimberly ^{[1
]}

Heinzen, Erin L. ^{[1
]}

Need, Anna C. ^{[1
]}

Cirulli, Elizabeth T. ^{[1
]}

Maia, Jessica M. ^{[1
]}

Dickson, Samuel P. ^{[1
]}

Zhu, Mingfu ^{[1
]}

Singh, Abanish ^{[1
]}

Allen, Andrew S. ^{[2
]}

Goldstein, David B. ^{[1
]}

机构：

[1] Duke Univ Sch Med, Ctr Human Genome Variat, Durham, NC 27708 USA

[2] Duke Univ Sch Med, Dept Biostat & Bioinformat, Durham, NC 27708 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 14期

基金：

比尔及梅琳达.盖茨基金会;

关键词：

STRUCTURAL VARIATION; ASSOCIATION; ALIGNMENT; MAP;

D O I：

10.1093/bioinformatics/btr317

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits. We illustrate the annotation features of SVA using two simple examples of sequenced genomes that harbor Mendelian mutations.

引用

页码：1998 / 2000

页数：3

共 24 条

[1] A map of human genome variation from population-scale sequencing
Altshuler, David
Durbin, Richard M.
Abecasis, Goncalo R.
Bentley, David R.
Chakravarti, Aravinda
Clark, Andrew G.
Collins, Francis S.
De la Vega, Francisco M.
Donnelly, Peter
Egholm, Michael
Flicek, Paul
Gabriel, Stacey B.
Gibbs, Richard A.
Knoppers, Bartha M.
Lander, Eric S.
Lehrach, Hans
Mardis, Elaine R.
McVean, Gil A.
Nickerson, DebbieA.
Peltonen, Leena
Schafer, Alan J.
Sherry, Stephen T.
Wang, Jun
Wilson, Richard K.
Gibbs, Richard A.
Deiros, David
Metzker, Mike
Muzny, Donna
Reid, Jeff
Wheeler, David
Wang, Jun
Li, Jingxiang
Jian, Min
Li, Guoqing
Li, Ruiqiang
Liang, Huiqing
Tian, Geng
Wang, Bo
Wang, Jian
Wang, Wei
Yang, Huanming
Zhang, Xiuqing
Zheng, Huisong
Lander, Eric S.
Altshuler, David L.
Ambrogio, Lauren
Bloom, Toby
Cibulskis, Kristian
Fennell, Tim J.
Gabriel, Stacey B.
[J]. NATURE, 2010, 467 (7319) : 1061 - 1073
[2] Gene Ontology: tool for the unification of biology
Ashburner, M
Ball, CA
Blake, JA
Botstein, D
Butler, H
Cherry, JM
Davis, AP
Dolinski, K
Dwight, SS
Eppig, JT
Harris, MA
Hill, DP
Issel-Tarver, L
Kasarskis, A
Lewis, S
Matese, JC
Richardson, JE
Ringwald, M
Rubin, GM
Sherlock, G
[J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
[3] Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, David R.
Balasubramanian, Shankar
Swerdlow, Harold P.
Smith, Geoffrey P.
Milton, John
Brown, Clive G.
Hall, Kevin P.
Evers, Dirk J.
Barnes, Colin L.
Bignell, Helen R.
Boutell, Jonathan M.
Bryant, Jason
Carter, Richard J.
Cheetham, R. Keira
Cox, Anthony J.
Ellis, Darren J.
Flatbush, Michael R.
Gormley, Niall A.
Humphray, Sean J.
Irving, Leslie J.
Karbelashvili, Mirian S.
Kirk, Scott M.
Li, Heng
Liu, Xiaohai
Maisinger, Klaus S.
Murray, Lisa J.
Obradovic, Bojan
Ost, Tobias
Parkinson, Michael L.
Pratt, Mark R.
Rasolonjatovo, Isabelle M. J.
Reed, Mark T.
Rigatti, Roberto
Rodighiero, Chiara
Ross, Mark T.
Sabot, Andrea
Sankar, Subramanian V.
Scally, Aylwyn
Schroth, Gary P.
Smith, Mark E.
Smith, Vincent P.
Spiridou, Anastassia
Torrance, Peta E.
Tzonev, Svilen S.
Vermaas, Eric H.
Walter, Klaudia
Wu, Xiaolin
Zhang, Lu
Alam, Mohammed D.
Anastasi, Carole
[J]. NATURE, 2008, 456 (7218) : 53 - 59
[4] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Birney, Ewan
Stamatoyannopoulos, John A.
Dutta, Anindya
Guigo, Roderic
Gingeras, Thomas R.
Margulies, Elliott H.
Weng, Zhiping
Snyder, Michael
Dermitzakis, Emmanouil T.
Stamatoyannopoulos, John A.
Thurman, Robert E.
Kuehn, Michael S.
Taylor, Christopher M.
Neph, Shane
Koch, Christoph M.
Asthana, Saurabh
Malhotra, Ankit
Adzhubei, Ivan
Greenbaum, Jason A.
Andrews, Robert M.
Flicek, Paul
Boyle, Patrick J.
Cao, Hua
Carter, Nigel P.
Clelland, Gayle K.
Davis, Sean
Day, Nathan
Dhami, Pawandeep
Dillon, Shane C.
Dorschner, Michael O.
Fiegler, Heike
Giresi, Paul G.
Goldy, Jeff
Hawrylycz, Michael
Haydock, Andrew
Humbert, Richard
James, Keith D.
Johnson, Brett E.
Johnson, Ericka M.
Frum, Tristan T.
Rosenzweig, Elizabeth R.
Karnani, Neerja
Lee, Kirsten
Lefebvre, Gregory C.
Navas, Patrick A.
Neri, Fidencio
Parker, Stephen C. J.
Sabo, Peter J.
Sandstrom, Richard
Shafer, Anthony
[J]. NATURE, 2007, 447 (7146) : 799 - 816
[5] Chen K, 2009, NAT METHODS, V6, P677, DOI [10.1038/NMETH.1363, 10.1038/nmeth.1363]
[6] Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
Choi, Murim
Scholl, Ute I.
Ji, Weizhen
Liu, Tiewen
Tikhonova, Irina R.
Zumbo, Paul
Nayir, Ahmet
Bakkaloglu, Aysin
Ozen, Seza
Sanjad, Sami
Nelson-Williams, Carol
Farhi, Anita
Mane, Shrikant
Lifton, Richard P.
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (45) : 19096 - 19101
[7] Savant: genome browser for high-throughput sequencing data
Fiume, Marc
Williams, Vanessa
Brook, Andrew
Brudno, Michael
[J]. BIOINFORMATICS, 2010, 26 (16) : 1938 - 1944
[8] Ensembl's 10th year
Flicek, Paul
Aken, Bronwen L.
Ballester, Benoit
Beal, Kathryn
Bragin, Eugene
Brent, Simon
Chen, Yuan
Clapham, Peter
Coates, Guy
Fairley, Susan
Fitzgerald, Stephen
Fernandez-Banet, Julio
Gordon, Leo
Graef, Stefan
Haider, Syed
Hammond, Martin
Howe, Kerstin
Jenkinson, Andrew
Johnson, Nathan
Kaehaeri, Andreas
Keefe, Damian
Keenan, Stephen
Kinsella, Rhoda
Kokocinski, Felix
Koscielny, Gautier
Kulesha, Eugene
Lawson, Daniel
Longden, Ian
Massingham, Tim
McLaren, William
Megy, Karine
Overduin, Bert
Pritchard, Bethan
Rios, Daniel
Ruffier, Magali
Schuster, Michael
Slater, Guy
Smedley, Damian
Spudich, Giulietta
Tang, Y. Amy
Trevanion, Stephen
Vilella, Albert
Vogel, Jan
White, Simon
Wilder, Steven P.
Zadissa, Amonida
Birney, Ewan
Cunningham, Fiona
Dunham, Ian
Durbin, Richard
[J]. NUCLEIC ACIDS RESEARCH, 2010, 38 : D557 - D562
[9] A second generation human haplotype map of over 3.1 million SNPs
Frazer, Kelly A.
Ballinger, Dennis G.
Cox, David R.
Hinds, David A.
Stuve, Laura L.
Gibbs, Richard A.
Belmont, John W.
Boudreau, Andrew
Hardenbol, Paul
Leal, Suzanne M.
Pasternak, Shiran
Wheeler, David A.
Willis, Thomas D.
Yu, Fuli
Yang, Huanming
Zeng, Changqing
Gao, Yang
Hu, Haoran
Hu, Weitao
Li, Chaohua
Lin, Wei
Liu, Siqi
Pan, Hao
Tang, Xiaoli
Wang, Jian
Wang, Wei
Yu, Jun
Zhang, Bo
Zhang, Qingrun
Zhao, Hongbin
Zhao, Hui
Zhou, Jun
Gabriel, Stacey B.
Barry, Rachel
Blumenstiel, Brendan
Camargo, Amy
Defelice, Matthew
Faggart, Maura
Goyette, Mary
Gupta, Supriya
Moore, Jamie
Nguyen, Huy
Onofrio, Robert C.
Parkin, Melissa
Roy, Jessica
Stahl, Erich
Winchester, Ellen
Ziaugra, Liuda
Altshuler, David
Shen, Yan
[J]. NATURE, 2007, 449 (7164) : 851 - U3
[10] WGAViewer: Software for genomic annotation of whole genome association studies
Ge, Dongliang
Zhang, Kunlin
Need, Anna C.
Martin, Olivier
Fellay, Jacques
Urban, Thomas J.
Telenti, Amalio
Goldstein, David B.
[J]. GENOME RESEARCH, 2008, 18 (04) : 640 - 643

← 1 2 3 →